An ion trap mass spectrometer which uses an ion trap capable of capturing ions by the effect of a radio-frequency electric field has been known as one type of mass spectrometer. A typically used ion trap is a three-dimensional quadrupole ion trap, which includes a pair of endcap electrodes facing each other across a doughnut-shaped ring electrode. Another commonly known type of ion trap is a linear ion trap, which includes four rod electrodes arranged parallel to each other, with two endcap electrodes respectively arranged on the outside of the two ends of those rod electrodes. The following description deals with the case of an ion trap mass spectrometer using a three-dimensional quadrupole ion trap unless otherwise noted.
Normally, in an ion trap mass spectrometer, a radio-frequency voltage is applied to the ring electrode while the pair of endcap electrodes are maintained at a potential of 0 V, to create a radio-frequency quadrupole electric field within the inner space of the ion trap and capture ions by the effect of this electric field. It has been commonly known that the behavior of the ions captured within the inner space of the ion trap can be expressed by the Mathieu equation. If the amplitude value of the radio-frequency voltage applied to the ring electrode is gradually increased under the condition that ions are captured within the inner space of the ion trap, the trajectories of the ions become unstable in ascending order of mass-to-charge ratio, and are eventually ejected to the outside through an opening bored in one of the endcap electrodes. By employing this principle, it is possible to separate ions from each other by their mass-to-charge ratios or selectively maintain an ion having a specific mass-to-charge ratio within the inner space of the ion trap (see Non-Patent Literature 1 or other documents).
In many of the conventionally used ion trap mass spectrometers, the radio-frequency voltage applied to the ring electrode is a sinusoidal voltage. Meanwhile, an ion trap mass spectrometer in which a rectangular radio-frequency voltage is applied to the ring electrode is also known, as disclosed in Non-Patent Literature 2 or other documents. Such an ion trap has conventionally been called the “digital ion trap”. A mass spectrometer using a digital ion trap can separate ions from each other by their mass-to-charge ratios or selectively maintain an ion having a specific mass-to-charge ratio, by controlling the frequency of the rectangular voltage applied to the ring electrode while maintaining the voltage value (pulse-height value) of the rectangular voltage.
In the previously described types of ion trap mass spectrometers, an MS/MS analysis or MS' analysis can be performed as follows: Various ions of sample origin are temporarily captured within the ion trap. Among those ions, a target ion with a specific mass-to-charge ratio is selectively maintained within the inner space of the ion trap. This ion is used as a precursor ion and dissociated into product ions within the inner space of the ion trap. The product ions are individually separated by mass and detected. The most commonly used method for dissociating an ion is the collision induced dissociation (CID), in which the dissociation of an ion is promoted by making the ion collide with gas (normally, inert gas). There are also other techniques: a hydrogen radical attachment dissociation (HAD), in which the dissociation of an ion is promoted by irradiation with hydrogen radicals, which are uncharged particles; an electron transfer dissociation (ETD) or electron capture dissociation (ECD), in which the dissociation of an ion is promoted by a supply of electrons; and an infrared multi-photon dissociation (IRMPD), in which the dissociation of an ion is promoted by irradiation with infrared laser light (see Non-Patent Literature 3, Patent Literature 1, or other documents).
It has been commonly known that dissociating the same precursor ion by a different dissociation technique produces different kinds of product ions and consequently yields a different kind of structural information on the ion. For example, according to Non-Patent Literature 4, using the CID for a glycopeptide in which a sugar chain is bound to a peptide yields information on the structure of the sugar chain, whereas using the ETD yields information on the peptide structure and information on the binding site of the sugar chain. Accordingly, it is possible to collectively obtain information on the sugar-chain structure, peptide structure and sugar-chain binding site by combining the result of an MSn analysis using the CID and that of an MSn analysis using the ETD, which allows for a detailed structural analysis of the glycopeptide. This holds true for not only the combination of CID and ETD but also for other combinations, such as the CID and ECD, or CID and HAD.
The previously described MSn analysis has the following problem:
Although any of the previously described techniques can induce dissociation of an ion, those techniques are significantly different in dissociation efficiency. For example, the target precursor ion can be almost entirely dissociated by changing the voltage or reaction time in the ion-exciting operation in the case of the CID, or by changing the laser power or period of irradiation with the laser light in the case of the IRMPD. In other words, the precursor-ion dissociation efficiency is almost 100%. By comparison, the precursor-ion dissociation efficiency in HAD, ECD and ETD is lower than in CID or other techniques. For example, Non-Patent Literature 5 reports that the precursor-ion dissociation efficiency in ECD is approximately 15% for peptides and approximately 30% for proteins.
Using such a dissociation technique whose precursor-ion dissociation efficiency is low means a corresponding decrease in the amount of product ions to be generated, which leads to a decrease in the detection sensitivity and in the signal-to-noise (SN) ratio of the signals, if obtained, originating from the product ions. Therefore, for example, it is possible that a peak corresponding to a product ion whose amount of generation is originally small becomes unobservable on the MS/MS spectrum.
FIGS. 7A and 7B show a comparison between an MS/MS spectrum obtained when CID was used as the ion dissociation technique, and one obtained when HAD was used. As shown in FIG. 7A, when CID is used, the signal intensity of the precursor ion becomes significantly low, while those of the product ions generally become high. On the other hand, as shown in FIG. 7B, when HAD is used, a considerable amount of precursor ion remains undissociated, so that the signal intensity of the precursor ion becomes high, while those of the product ions generally become low.
In order to improve the detection sensitivity and SN ratio of the signal, it is necessary to repeat the MSn analysis on the same sample multiple times and accumulate signal intensities respectively obtained in the individual MSn analyses. However, such an analysis consumes a considerable amount of sample and may exhaust the sample. Furthermore, if a sufficient amount of sample is not available, it is impossible obtain an MS/MS spectrum with a high level of quality. This may cause problems in the structural analysis of the target component or other tasks.